That is a good document, but as I see it has been written from the point-of-view of an US based law firm, it holds only in the US (just as it says on the final caption, "there's no such thing as a world-wide patent")

Also, the point-of-view in the document is on the decision of commercial entity, whether to patent or to GPL a feature/program.

As long as you are not going to make money/commercialize on a product, it is always allowed to make a clean-room implementation of a program/feature. That right cannot be taken away from you.
(this means, of course, that you write it yourself from scratch or use for example GPL'ed components. No peeking in the source code of the original implementation allowed )